Variant report

Variant	rs11968879
Chromosome Location	chr6:150161242-150161243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr6:150161242-150162537	SK-N-SH	brain:	n/a	chr6:150161622-150161629
2	NRF1	chr6:150161214-150161247	HepG2	liver:	n/a	n/a
3	STAT3	chr6:150161102-150161484	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:150160714..150164051-chr6:150166023..150170073,4	MCF-7	breast:
2	chr6:150159974..150162736-chr6:150163125..150166318,3	K562	blood:
3	chr6:150153688..150155920-chr6:150160413..150161947,2	MCF-7	breast:
4	chr6:150160122..150165164-chr6:150183114..150187569,12	MCF-7	breast:
5	chr6:150159974..150162858-chr6:150163125..150167505,4	K562	blood:

Variant related genes	Relation type
LRP11	TF binding region
ENSG00000120256	Chromatin interaction
ENSG00000268592	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11961510	1.00[JPT][hapmap]
rs11961527	1.00[JPT][hapmap]
rs11963771	1.00[JPT][hapmap]
rs11966407	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11968728	1.00[JPT][hapmap]
rs17078923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17088269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs3806983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs60226016	0.87[EUR][1000 genomes]
rs60328093	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60475279	1.00[ASN][1000 genomes]
rs60640690	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60981297	0.87[EUR][1000 genomes]
rs61292046	0.87[EUR][1000 genomes]
rs6899595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6919437	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73612418	0.87[EUR][1000 genomes]
rs73612420	0.87[EUR][1000 genomes]
rs7744111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7753340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7762484	0.87[EUR][1000 genomes]
rs7770995	1.00[JPT][hapmap]
rs9478983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs9478993	0.87[EUR][1000 genomes]
rs9478994	0.87[EUR][1000 genomes]
rs9478995	0.87[EUR][1000 genomes]
rs9688944	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1803291	chr6:150018508-150164190	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv886763	chr6:150091219-150174507	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150073800-150182400	Weak transcription	Fetal Brain Male	brain
2	chr6:150094400-150167200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:150105800-150176400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:150112600-150167200	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:150119000-150164000	Weak transcription	Right Ventricle	heart
6	chr6:150120000-150164600	Weak transcription	Fetal Kidney	kidney
7	chr6:150132800-150161800	Weak transcription	Fetal Lung	lung
8	chr6:150133200-150161800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:150133200-150162000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:150135000-150161600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:150141400-150167200	Weak transcription	Right Atrium	heart
12	chr6:150143600-150161600	Weak transcription	Left Ventricle	heart
13	chr6:150146200-150167000	Weak transcription	Psoas Muscle	Psoas
14	chr6:150147800-150163600	Weak transcription	Fetal Brain Female	brain
15	chr6:150150600-150166400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:150151200-150161600	Weak transcription	Stomach Mucosa	stomach
17	chr6:150152400-150165400	Weak transcription	HSMMtube	muscle
18	chr6:150152600-150161600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:150152800-150161600	Weak transcription	Pancreas	Pancrea
20	chr6:150152800-150161800	Weak transcription	HSMM	muscle
21	chr6:150152800-150172600	Weak transcription	Aorta	Aorta
22	chr6:150153000-150163600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:150153000-150167000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:150153000-150167800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:150153200-150161600	Weak transcription	Brain Substantia Nigra	brain
26	chr6:150155800-150182600	Weak transcription	Dnd41	blood
27	chr6:150156400-150168400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:150157600-150161600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:150157600-150161600	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:150157600-150167000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:150158000-150161400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:150158600-150161600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:150158600-150161800	Weak transcription	Brain Angular Gyrus	brain
34	chr6:150158600-150163800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:150158600-150165400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:150158600-150167200	Weak transcription	Adipose Nuclei	Adipose
37	chr6:150158800-150161600	Weak transcription	Liver	Liver
38	chr6:150158800-150161600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr6:150158800-150161600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:150158800-150161600	Weak transcription	Gastric	stomach
41	chr6:150158800-150161600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:150158800-150161600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr6:150158800-150161600	Weak transcription	Hela-S3	cervix
44	chr6:150158800-150163400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:150158800-150176400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:150159000-150161600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:150159000-150161600	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:150159000-150161600	Weak transcription	Placenta	Placenta
49	chr6:150159000-150161600	Weak transcription	Lung	lung
50	chr6:150159000-150161600	Weak transcription	HepG2	liver

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